The two-time Masters champion will miss the event for the first time since he made his debut at Augusta National in 1978.
Along with Ballesteros' Masters victories in 1980 and 1983, the 46-year-old Spaniard has won the British Open three times.
Ballesteros last made the cut at Augusta National in 1996 when he finished 43rd.
The Masters will be contested from April 8-11. Canada's Mike Weir is the defending champion.